LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -72.584394 0.0000000) to (41.904529 72.584394 6.2700239) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6289666 5.7775740 6.2700239 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.584394 0.0000000) to (41.904529 72.584394 6.2700239) create_atoms CPU = 0.011 seconds 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6289666 5.7775740 6.2700239 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.584394 0.0000000) to (41.904529 72.584394 6.2700239) create_atoms CPU = 0.010 seconds 1610 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 49 3 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 3192 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_227887284491_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.762 | 5.762 | 5.762 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11234.184 0 -11234.184 1128.0035 28 0 -11269.243 0 -11269.243 -6522.4922 Loop time of 13.1598 on 1 procs for 28 steps with 3192 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11234.1844830552 -11269.2318861919 -11269.2428601041 Force two-norm initial, final = 45.929872 0.29280962 Force max component initial, final = 8.6243851 0.045531748 Final line search alpha, max atom move = 1.0000000 0.045531748 Iterations, force evaluations = 28 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.092 | 13.092 | 13.092 | 0.0 | 99.48 Neigh | 0.040513 | 0.040513 | 0.040513 | 0.0 | 0.31 Comm | 0.010798 | 0.010798 | 0.010798 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01675 | | | 0.13 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8669.00 ave 8669 max 8669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 247256.0 ave 247256 max 247256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 247256 Ave neighs/atom = 77.461153 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.768 | 5.768 | 5.768 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -11269.243 0 -11269.243 -6522.4922 38141.996 31 0 -11269.444 0 -11269.444 -2035.4151 38021.184 Loop time of 1.77462 on 1 procs for 3 steps with 3192 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11269.2428601041 -11269.4439974526 -11269.4441855309 Force two-norm initial, final = 177.15566 0.31915315 Force max component initial, final = 137.01572 0.080728558 Final line search alpha, max atom move = 0.00035659855 2.8787687e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7669 | 1.7669 | 1.7669 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014119 | 0.0014119 | 0.0014119 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006342 | | | 0.36 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8672.00 ave 8672 max 8672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 247336.0 ave 247336 max 247336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 247336 Ave neighs/atom = 77.486216 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.906 | 5.906 | 5.906 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11269.444 0 -11269.444 -2035.4151 Loop time of 6.806e-06 on 1 procs for 0 steps with 3192 atoms 176.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.806e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8672.00 ave 8672 max 8672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 247372.0 ave 247372 max 247372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 247372 Ave neighs/atom = 77.497494 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.906 | 5.906 | 5.906 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -11269.444 -11269.444 41.848827 145.16879 6.2584832 -2035.4151 -2035.4151 -3.3973027 -6101.7325 -1.1154645 2.3053377 1119.9678 Loop time of 6.946e-06 on 1 procs for 0 steps with 3192 atoms 316.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.946e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8672.00 ave 8672 max 8672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 123686.0 ave 123686 max 123686 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 247372.0 ave 247372 max 247372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 247372 Ave neighs/atom = 77.497494 Neighbor list builds = 0 Dangerous builds = 0 3192 -11269.4441855309 eV 2.30533772533968 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16